TissueNets HowToBuild
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| − | In order to use the TissueNets | + | == TissueNets System == |
| + | |||
| + | In order to use the programs included in the TissueNets system with its python GUI, we need to have the following programs: | ||
{| border="1" | {| border="1" | ||
| Line 6: | Line 8: | ||
|- | |- | ||
| TissueNets | | TissueNets | ||
| − | | Displays biological networks, Creates Cluto files | + | | Main TissueNets module, Displays biological networks, Creates Cluto files |
| − | | tissuenets | + | | tissuenets/tissuenets |
| − | | | + | | tissuenets.cpp |
|- | |- | ||
| − | | | + | | read_cell_types |
| − | | | + | | Extracts all cell types from the input file dynamically |
| − | | tissuenets//tissuenets | + | | tissuenets/read_cell_types |
| − | | (tissuenets.cpp) | + | | read_cell_types.cpp |
| + | |- | ||
| + | | readtextfile | ||
| + | | Reads text file and converts it into the XML that could be used by the main module | ||
| + | | tissuenets/readtextfile | ||
| + | | readtextfile.cpp | ||
| + | |- | ||
| + | | defineNodes | ||
| + | | Creates Nodes of the network | ||
| + | | tissuenets/XQUERY-programs | ||
| + | | defineNodes.XQUERY (no need to build) | ||
| + | |- | ||
| + | | kneighbor | ||
| + | | Creates links based on k-nearest neighbor algorithm (with exact solution) | ||
| + | | tissuenets/XQUERY-programs | ||
| + | | kneighbor.XQUERY (no need to build) | ||
| + | |- | ||
| + | | defineNetwork | ||
| + | | Combines nodes and links and forms a network in [[http://www.cs.rpi.edu/~puninj/XGMML/ XGMML]] form | ||
| + | | tissuenets/XQUERY-programs | ||
| + | | defineNetwork.XQUERY (no need to build) | ||
| + | |- | ||
| + | | defineHistogram | ||
| + | | Creates histogram data by using the given feature name and the input file (which is formatted in XML) | ||
| + | | tissuenets/XQUERY-programs | ||
| + | | defineHistogram.XQUERY (no need to build) | ||
| + | |- | ||
| + | | BioNet | ||
| + | | This is the older version of the main TissueNets module. We use it to create minimum spanning trees (will be removed in the near future) | ||
| + | | tissuenets/ | ||
| + | | bionet.cpp | ||
| + | |- | ||
| + | | tissuenets-py | ||
| + | | python GUI for all the programs in the TissueNets system. | ||
| + | | tissuenets/python-GUI-and-other-windows-programs | ||
| + | | tissuenets-py.py (no need to build) | ||
|} | |} | ||
| − | + | == How to Run XQUERY Programs == | |
| − | + | * Install Java | |
| − | + | * Download and install Saxon-B 9.1 from: | |
| − | + | http://saxon.sourceforge.net/ (Click on “Download for Java") | |
| − | + | ||
| − | + | ||
| − | Note that | + | Note that we have included the required Jar files (saxon9 and others) in \trunk\tissuenets\python-GUI-and-other-windows-programs directory. They should be sufficient to run XQUERY programs. |
| − | DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE | + | (DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE.) |
| − | + | * Set the CLASSPATH accordingly so that the required jar files can be found. (If the Jar files are in the current directory, including it in the CLASSPATH will do the job) | |
| − | + | * Download and Install Python from http://www.python.org/ | |
| − | + | == To run TissueNets with its Python Interface == | |
| − | + | * Change the directory to where you have all the files | |
| − | + | * Type : python tissuenets-py.py | |
| − | python | + | |
Latest revision as of 17:46, 25 August 2009
TissueNets System
In order to use the programs included in the TissueNets system with its python GUI, we need to have the following programs:
| Module Name | What it does | Location | What to Build |
|---|---|---|---|
| TissueNets | Main TissueNets module, Displays biological networks, Creates Cluto files | tissuenets/tissuenets | tissuenets.cpp |
| read_cell_types | Extracts all cell types from the input file dynamically | tissuenets/read_cell_types | read_cell_types.cpp |
| readtextfile | Reads text file and converts it into the XML that could be used by the main module | tissuenets/readtextfile | readtextfile.cpp |
| defineNodes | Creates Nodes of the network | tissuenets/XQUERY-programs | defineNodes.XQUERY (no need to build) |
| kneighbor | Creates links based on k-nearest neighbor algorithm (with exact solution) | tissuenets/XQUERY-programs | kneighbor.XQUERY (no need to build) |
| defineNetwork | Combines nodes and links and forms a network in [XGMML] form | tissuenets/XQUERY-programs | defineNetwork.XQUERY (no need to build) |
| defineHistogram | Creates histogram data by using the given feature name and the input file (which is formatted in XML) | tissuenets/XQUERY-programs | defineHistogram.XQUERY (no need to build) |
| BioNet | This is the older version of the main TissueNets module. We use it to create minimum spanning trees (will be removed in the near future) | tissuenets/ | bionet.cpp |
| tissuenets-py | python GUI for all the programs in the TissueNets system. | tissuenets/python-GUI-and-other-windows-programs | tissuenets-py.py (no need to build) |
How to Run XQUERY Programs
- Install Java
- Download and install Saxon-B 9.1 from:
http://saxon.sourceforge.net/ (Click on “Download for Java")
Note that we have included the required Jar files (saxon9 and others) in \trunk\tissuenets\python-GUI-and-other-windows-programs directory. They should be sufficient to run XQUERY programs.
(DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE.)
- Set the CLASSPATH accordingly so that the required jar files can be found. (If the Jar files are in the current directory, including it in the CLASSPATH will do the job)
- Download and Install Python from http://www.python.org/
To run TissueNets with its Python Interface
- Change the directory to where you have all the files
- Type : python tissuenets-py.py
